MERFISH Report

1. Overview

1.1 Sample Information

A brief sample information is generated from the submission table for the following analysis.

Sample Index and Basic Information
Batch Index Genotype Time Data Path Region
1 tBHP_4_0 tBHP 4 202402021652_20240202MFisherBHP4hxm500VZG191x01_VMSC00101 region_0
1 tBHP_4_1 tBHP 4 202402021652_20240202MFisherBHP4hxm500VZG191x01_VMSC00101 region_1
1 PBS_4_0 PBS 4 202402021652_20240202MFisherBHP4hxm500VZG191x01_VMSC00101 region_2
1 PBS_4_1 PBS 4 202402021652_20240202MFisherBHP4hxm500VZG191x01_VMSC00101 region_3
2 PBS_24_0 PBS 24 202402021711_20240202MFisherBHP24hxm500VZG191x02_VMSC05201 region_0
2 PBS_24_1 PBS 24 202402021711_20240202MFisherBHP24hxm500VZG191x02_VMSC05201 region_1
2 tBHP_24_0 tBHP 24 202402021711_20240202MFisherBHP24hxm500VZG191x02_VMSC05201 region_2
2 tBHP_24_1 tBHP 24 202402021711_20240202MFisherBHP24hxm500VZG191x02_VMSC05201 region_3

1.2 Data Quality

1.2.1 MERSCOPE Data Quality Summary

The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.

Generally, log10 transcript count > 5.0 in most area can be considered as a good quality standard.

Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

1.2.2 Transcript Count Level

Transcript counts on each sample

Transcript counts on each sample

2. Data Processing

2.1 Cell Segmentation

Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.

To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 1800], and the gene count per cell > 25.

Outliers were filtered from the data, and the qualified cells count is presented in the following table. The identified cells after filtering are listed in the following table. In total, the study identified 122328 cells across 8 samples.

Segmented Cell Count in each Samples
Sample Index Cell Count
tBHP_4_1 20452
tBHP_4_0 18804
tBHP_24_1 18206
PBS_4_1 16603
PBS_24_1 13900
tBHP_24_0 13452
PBS_24_0 12141
PBS_4_0 8770
Identified Cell Spatial Overview on all Samples

Identified Cell Spatial Overview on all Samples

–>

2.2 Cell Annotation

We use a recent published tool: Map My Cell to perform cell type annotations for each cell. It is a high resolution cell type annotator build by Alan Institude, with nested levels of classification including 34 classes and 338 subclasses.

The taxonomy is based on the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3)[https://doi.org/10.1016/j.cell.2020.04.007]. Part of the used abbreviations is list in the supplementary Abbreviation. Otherwise can be found in CCFv3 paper.

With the annotation, we can identify and plot the selected types of cells in each sample, and exclude uncertaine cells by bootstrapping probability < 0.9.

2.2.1 Cell Type Spatial Map

2.2.2 Endothelia & Microglia Spatial Map

2.2.3 Cell Type Count Table

Cell Type Count
PBS_24 PBS_4 tBHP_24 tBHP_4
Astrocyte 2139 1856 2827 3004
Endo 603 678 1021 989
L2/3 Glut 547 317 903 1290
L4/5 Glut 1385 733 2010 2090
L5 Glut 563 501 901 1162
L6 Glut 299 205 404 718
L6b Glut 922 611 1223 1325
Microglia 445 518 581 1099
OPC 398 433 534 842
Oligo 2095 2308 3535 3061
Peri 319 296 513 601
STR D1 GABA 430 1763 609 2901
STR D2 GABA 824 2362 1043 3660
TH Glut 1117 459 726 46

3. Gene Differentiation

3.1 Data Mining for Ischemia & Hypoxia

We found the ischemia and hypoxia mouse gene list by searching public mouse genome database Mouse Genome Informatics (MGI). It provided related gene list by matching terms from validated resources, such as gene ontology pathways.

Overall, 94 genes are found by ischemia term, and 349 genes are found in hypoxia.

Among those, 30 genes are both in ischemia & hypoxia pathway, which are: Ccl2, Epo, Pgf, Aifm1, Aqp3, Bcl2, Casp9, Casr, Cav1, Cav3, Egr1, Hk2, Hyou1, Kcnj8, Kcnj11, Mir874, Ndnf, Nfe2l2, Nol3, Nppc, P2rx2, Pik3cb, Pink1, Ptk2b, Rest, Rock2, Stat3, Tigar, Trem2, Trp53.

3.1.1 Ischemia Gene List

Type MGI.ID Symbol Name Chr Start End Build Strand Best.Match.Type Best.Match Match.Score
protein coding gene MGI:98259 Ccl2 C-C motif chemokine ligand 2 11 81926403 81928278 GRCm39
Disease Ortholog ischemia 4
protein coding gene MGI:108224 Ccl12 C-C motif chemokine ligand 12 11 81992671 81994225 GRCm39
Disease Ortholog ischemia 4
protein coding gene MGI:106639 Mthfr methylenetetrahydrofolate reductase 4 148123534 148144008 GRCm39
Disease Ortholog ischemia 4
lncRNA gene MGI:5595308 Cirpil cardiac ischemia reperfusion associated p53 interacting lncRNA 5 111638797 111640250 GRCm39
Name cardiac ischemia reperfusion associated p53 interacting lncRNA 3
QTL MGI:3795764 Lsq1 loss of tissue after ischemia QTL 1 7 syntenic NA GRCm39 null Name loss of tissue after ischemia QTL 1 3
protein coding gene MGI:108448 Angpt1 angiopoietin 1 15 42288119 42540373 GRCm39
Disease Ortholog brain ischemia (subterm of ischemia) 3
protein coding gene MGI:96819 Anxa1 annexin A1 19 20350798 20368035 GRCm39
Disease Ortholog brain ischemia (subterm of ischemia) 3
protein coding gene MGI:108052 Bcl2l2 BCL2-like 2 14 55120900 55125691 GRCm39
Disease Ortholog transient cerebral ischemia (subterm of ischemia) 3
protein coding gene MGI:1339751 Csf3 colony stimulating factor 3 (granulocyte) 11 98592089 98594455 GRCm39
Disease Ortholog brain ischemia (subterm of ischemia) 3
protein coding gene MGI:1859388 Dll4 delta like canonical Notch ligand 4 2 119156265 119166147 GRCm39
Disease Ortholog limb ischemia (subterm of ischemia) 3
protein coding gene MGI:95407 Epo erythropoietin 5 137481282 137484078 GRCm39
Disease Ortholog limb ischemia (subterm of ischemia) 3
protein coding gene MGI:95412 Ercc1 excision repair cross-complementing rodent repair deficiency, complementation group 1 7 19079016 19090449 GRCm39
Disease Ortholog transient cerebral ischemia (subterm of ischemia) 3
protein coding gene MGI:99253 Etv2 ets variant 2 7 30333041 30335277 GRCm39
Disease Ortholog limb ischemia (subterm of ischemia) 3
protein coding gene MGI:1891012 F12 coagulation factor XII (Hageman factor) 13 55565771 55574606 GRCm39
Disease Ortholog transient cerebral ischemia (subterm of ischemia) 3
protein coding gene MGI:95515 Fgf1 fibroblast growth factor 1 18 38971726 39062525 GRCm39
Disease Ortholog brain ischemia (subterm of ischemia) 3
protein coding gene MGI:95791 Got1 glutamic-oxaloacetic transaminase 1, soluble 19 43488191 43513044 GRCm39
Disease Ortholog transient cerebral ischemia (subterm of ischemia) 3
protein coding gene MGI:96079 Hgf hepatocyte growth factor 5 16758493 16825150 GRCm39
Disease Ortholog limb ischemia (subterm of ischemia) 3
protein coding gene MGI:96244 Hspa1a heat shock protein 1A 17 35188335 35191132 GRCm39
Disease Ortholog brain ischemia (subterm of ischemia) 3
protein coding gene MGI:99517 Hspa1b heat shock protein 1B 17 35175412 35178214 GRCm39
Disease Ortholog brain ischemia (subterm of ischemia) 3
protein coding gene MGI:96432 Igf1 insulin-like growth factor 1 10 87694127 87772904 GRCm39
Disease Ortholog brain ischemia (subterm of ischemia) 3
protein coding gene MGI:96547 Il1rn interleukin 1 receptor antagonist 2 24226872 24241503 GRCm39
Disease Ortholog transient cerebral ischemia (subterm of ischemia) 3
protein coding gene MGI:96949 Mdk midkine 2 91760149 91762348 GRCm39
Disease Ortholog brain ischemia (subterm of ischemia) 3
protein coding gene MGI:1929865 Nampt nicotinamide phosphoribosyltransferase 12 32870334 32903368 GRCm39
Disease Ortholog transient cerebral ischemia (subterm of ischemia) 3
protein coding gene MGI:97362 Nos3 nitric oxide synthase 3, endothelial cell 5 24569808 24589472 GRCm39
Disease Ortholog limb ischemia (subterm of ischemia) 3
protein coding gene MGI:105095 Pgf placental growth factor 12 85213411 85224559 GRCm39
Disease Ortholog brain ischemia (subterm of ischemia) 3
protein coding gene MGI:1860488 Proz protein Z, vitamin K-dependent plasma glycoprotein 8 13110914 13126026 GRCm39
Disease Ortholog brain ischemia (subterm of ischemia) 3
protein coding gene MGI:98278 Sele selectin, endothelial cell 1 163875773 163885246 GRCm39
Disease Ortholog brain ischemia (subterm of ischemia) 3
protein coding gene MGI:108080 Serpinf1 serine (or cysteine) peptidase inhibitor, clade F, member 1 11 75300855 75313449 GRCm39
Disease Ortholog transient cerebral ischemia (subterm of ischemia) 3
protein coding gene MGI:98351 Sod1 superoxide dismutase 1, soluble 16 90017650 90023221 GRCm39
Disease Ortholog transient cerebral ischemia (subterm of ischemia) 3
protein coding gene MGI:1095418 Tfpi tissue factor pathway inhibitor 2 84263199 84307119 GRCm39
Disease Ortholog transient cerebral ischemia (subterm of ischemia) 3
protein coding gene MGI:1926116 Abraxas2 BRISC complex subunit 7 132460954 132486840 GRCm39
Process response to ischemia 3
protein coding gene MGI:1349419 Aifm1 apoptosis-inducing factor, mitochondrion-associated 1 X 47563821 47602440 GRCm39
Process response to ischemia 3
protein coding gene MGI:1333777 Aqp3 aquaporin 3 4 41092724 41098183 GRCm39
Process response to ischemia 3
protein coding gene MGI:88138 Bcl2 B cell leukemia/lymphoma 2 1 106465908 106642004 GRCm39
Process response to ischemia 3
protein coding gene MGI:88139 Bcl2l1 BCL2-like 1 2 152622588 152673648 GRCm39
Process response to ischemia 3
protein coding gene MGI:1346013 Bves blood vessel epicardial substance 10 45211868 45248575 GRCm39
Process response to ischemia 3
protein coding gene MGI:88256 Camk2a calcium/calmodulin-dependent protein kinase II alpha 18 61058704 61121224 GRCm39
Process response to ischemia 3
protein coding gene MGI:1277950 Casp9 caspase 9 4 141520923 141543287 GRCm39
Process response to ischemia 3
protein coding gene MGI:1351351 Casr calcium-sensing receptor 16 36314058 36382503 GRCm39
Process response to ischemia 3
protein coding gene MGI:102709 Cav1 caveolin 1, caveolae protein 6 17306387 17341323 GRCm39
Process response to ischemia 3
protein coding gene MGI:107570 Cav3 caveolin 3 6 112436466 112449833 GRCm39
Process response to ischemia 3
protein coding gene MGI:1344418 Cib1 calcium and integrin binding 1 7 79876904 79882553 GRCm39
Process response to ischemia 3
protein coding gene MGI:1914829 Cpeb4 cytoplasmic polyadenylation element binding protein 4 11 31822211 31885634 GRCm39
Process response to ischemia 3
protein coding gene MGI:1339753 Csf1 colony stimulating factor 1 (macrophage) 3 107648364 107667785 GRCm39
Process response to ischemia 3
protein coding gene MGI:1339758 Csf1r colony stimulating factor 1 receptor 18 61238644 61264211 GRCm39
Process response to ischemia 3
protein coding gene MGI:1097153 Cx3cl1 C-X3-C motif chemokine ligand 1 8 95498808 95509055 GRCm39
Process response to ischemia 3
protein coding gene MGI:1333815 Cx3cr1 C-X3-C motif chemokine receptor 1 9 119877749 119897362 GRCm39
Process response to ischemia 3
protein coding gene MGI:1195261 Eef2k eukaryotic elongation factor-2 kinase 7 120442080 120506441 GRCm39
Process response to ischemia 3
protein coding gene MGI:95295 Egr1 early growth response 1 18 34994260 34998009 GRCm39
Process response to ischemia 3
protein coding gene MGI:1919643 Faim2 Fas apoptotic inhibitory molecule 2 15 99394893 99426046 GRCm39
Process response to ischemia 3
protein coding gene MGI:95713 Gja1 gap junction protein, alpha 1 10 56253297 56266519 GRCm39
Process response to ischemia 3
protein coding gene MGI:95720 Gjb2 gap junction protein, beta 2 14 57336059 57342159 GRCm39
Process response to ischemia 3
protein coding gene MGI:1354372 Gpr31b G protein-coupled receptor 31, D17Leh66b region 17 13270208 13271167 GRCm39
Process response to ischemia 3
protein coding gene MGI:96103 Hk1 hexokinase 1 10 62104634 62215687 GRCm39
Process response to ischemia 3
protein coding gene MGI:1315197 Hk2 hexokinase 2 6 82702006 82751435 GRCm39
Process response to ischemia 3
protein coding gene MGI:108030 Hyou1 hypoxia up-regulated 1 9 44290840 44303662 GRCm39
Process response to ischemia 3
protein coding gene MGI:1100508 Kcnj8 potassium inwardly-rectifying channel, subfamily J, member 8 6 142510563 142517340 GRCm39
Process response to ischemia 3
protein coding gene MGI:107501 Kcnj11 potassium inwardly rectifying channel, subfamily J, member 11 7 45746545 45750215 GRCm39
Process response to ischemia 3
protein coding gene MGI:1346867 Map2k2 mitogen-activated protein kinase kinase 2 10 80941749 80960531 GRCm39
Process response to ischemia 3
protein coding gene MGI:1346868 Map2k3 mitogen-activated protein kinase kinase 3 11 60822880 60843637 GRCm39
Process response to ischemia 3
protein coding gene MGI:1346870 Map2k6 mitogen-activated protein kinase kinase 6 11 110289948 110416348 GRCm39
Process response to ischemia 3
protein coding gene MGI:1346876 Map3k5 mitogen-activated protein kinase kinase kinase 5 10 19810218 20018499 GRCm39
Process response to ischemia 3
protein coding gene MGI:99458 Mef2c myocyte enhancer factor 2C 13 83652153 83815199 GRCm39
Process response to ischemia 3
miRNA gene MGI:3718564 Mir874 microRNA 874 13 58170939 58171014 GRCm39
Process response to ischemia 3
protein coding gene MGI:1928485 Mlycd malonyl-CoA decarboxylase 8 120121617 120137841 GRCm39
Process response to ischemia 3
protein coding gene MGI:1915419 Ndnf neuron-derived neurotrophic factor 6 65648595 65689307 GRCm39
Process response to ischemia 3
protein coding gene MGI:108420 Nfe2l2 nuclear factor, erythroid derived 2, like 2 2 75505857 75534985 GRCm39
Process response to ischemia 3
protein coding gene MGI:1925938 Nol3 nucleolar protein 3 (apoptosis repressor with CARD domain) 8 106002777 106008571 GRCm39
Process response to ischemia 3
protein coding gene MGI:97369 Nppc natriuretic peptide type C 1 86594015 86598295 GRCm39
Process response to ischemia 3
protein coding gene MGI:97373 Npr3 natriuretic peptide receptor 3 15 11839982 11907287 GRCm39
Process response to ischemia 3
protein coding gene MGI:103187 Nqo1 NAD(P)H dehydrogenase, quinone 1 8 108114857 108129838 GRCm39
Process response to ischemia 3
protein coding gene MGI:2665170 P2rx2 purinergic receptor P2X, ligand-gated ion channel, 2 5 110487678 110491078 GRCm39
Process response to ischemia 3
protein coding gene MGI:1338859 P2rx4 purinergic receptor P2X, ligand-gated ion channel 4 5 122845607 122867801 GRCm39
Process response to ischemia 3
protein coding gene MGI:1860055 Panx1 pannexin 1 9 14917081 14956774 GRCm39
Process response to ischemia 3
protein coding gene MGI:1890615 Panx2 pannexin 2 15 88943937 88957770 GRCm39
Process response to ischemia 3
protein coding gene MGI:1195265 Per2 period circadian clock 2 1 91343704 91387046 GRCm39
Process response to ischemia 3
protein coding gene MGI:1922019 Pik3cb phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta 9 98920455 99022264 GRCm39
Process response to ischemia 3
protein coding gene MGI:1916193 Pink1 PTEN induced putative kinase 1 4 138040720 138053618 GRCm39
Process response to ischemia 3
protein coding gene MGI:2145814 Ppif peptidylprolyl isomerase F (cyclophilin F) 14 25694578 25700892 GRCm39
Process response to ischemia 3
protein coding gene MGI:104908 Ptk2b PTK2 protein tyrosine kinase 2 beta 14 66390706 66518501 GRCm39
Process response to ischemia 3
protein coding gene MGI:1890564 Rcan1 regulator of calcineurin 1 16 92188839 92263057 GRCm39
Process response to ischemia 3
protein coding gene MGI:103290 Rela v-rel reticuloendotheliosis viral oncogene homolog A (avian) 19 5687511 5698158 GRCm39
Process response to ischemia 3
protein coding gene MGI:104897 Rest RE1-silencing transcription factor 5 77413338 77434279 GRCm39
Process response to ischemia 3
protein coding gene MGI:107926 Rock2 Rho-associated coiled-coil containing protein kinase 2 12 16944896 17037824 GRCm39
Process response to ischemia 3
protein coding gene MGI:1915596 Sirt5 sirtuin 5 13 43518972 43548679 GRCm39
Process response to ischemia 3
protein coding gene MGI:107996 Slc8a2 solute carrier family 8 (sodium/calcium exchanger), member 2 7 15863751 15894988 GRCm39
Process response to ischemia 3
protein coding gene MGI:1933154 Slc26a5 solute carrier family 26, member 5 5 22015653 22070602 GRCm39
Process response to ischemia 3
protein coding gene MGI:98354 Sos1 SOS Ras/Rac guanine nucleotide exchange factor 1 17 80701181 80787882 GRCm39
Process response to ischemia 3
protein coding gene MGI:107931 Sqstm1 sequestosome 1 11 50090193 50101654 GRCm39
Process response to ischemia 3
protein coding gene MGI:103038 Stat3 signal transducer and activator of transcription 3 11 100777632 100830447 GRCm39
Process response to ischemia 3
protein coding gene MGI:2442752 Tigar Trp53 induced glycolysis regulatory phosphatase 6 127062079 127086520 GRCm39
Process response to ischemia 3
protein coding gene MGI:1913150 Trem2 triggering receptor expressed on myeloid cells 2 17 48653429 48659304 GRCm39
Process response to ischemia 3
protein coding gene MGI:98834 Trp53 transformation related protein 53 11 69471185 69482699 GRCm39
Process response to ischemia 3
protein coding gene MGI:103149 Uchl1 ubiquitin carboxy-terminal hydrolase L1 5 66833464 66844577 GRCm39
Process response to ischemia 3

3.1.2 Hypoxia Gene List

Type MGI.ID Symbol Name Chr Start End Build Strand Best.Match.Type Best.Match Match.Score
protein coding gene MGI:106918 Hif1a hypoxia inducible factor 1, alpha subunit 12 73948149 73994304 GRCm39
Name hypoxia inducible factor 1, alpha subunit 3
protein coding gene MGI:2442345 Hif1an hypoxia-inducible factor 1, alpha subunit inhibitor 19 44551293 44564713 GRCm39
Name hypoxia-inducible factor 1, alpha subunit inhibitor 3
protein coding gene MGI:1859778 Hif3a hypoxia inducible factor 3, alpha subunit 7 16765432 16796352 GRCm39
Name hypoxia inducible factor 3, alpha subunit 3
protein coding gene MGI:1916823 Hilpda hypoxia inducible lipid droplet associated 6 29272487 29275445 GRCm39
Name hypoxia inducible lipid droplet associated 3
protein coding gene MGI:108030 Hyou1 hypoxia up-regulated 1 9 44290840 44303662 GRCm39
Name hypoxia up-regulated 1 3
protein coding gene MGI:1932286 Egln1 egl-9 family hypoxia-inducible factor 1 8 125635326 125676063 GRCm39
Name egl-9 family hypoxia-inducible factor 1 3
protein coding gene MGI:1932287 Egln2 egl-9 family hypoxia-inducible factor 2 7 26858083 26866227 GRCm39
Name egl-9 family hypoxia-inducible factor 2 3
protein coding gene MGI:1932288 Egln3 egl-9 family hypoxia-inducible factor 3 12 54225767 54250646 GRCm39
Name egl-9 family hypoxia-inducible factor 3 3
protein coding gene MGI:3845761 Methig1 methyltransferase hypoxia inducible domain containing 1 15 100251081 100282316 GRCm39
Name methyltransferase hypoxia inducible domain containing 1 3
protein coding gene MGI:109169 Epas1 endothelial PAS domain protein 1 17 87061292 87140838 GRCm39
Synonym hypoxia inducible transcription factor 2alpha 3
protein coding gene MGI:1930666 Higd1a HIG1 domain family, member 1A 9 121677623 121686862 GRCm39
Protein Domain Hypoxia induced protein, domain 3
protein coding gene MGI:1922939 Higd1b HIG1 domain family, member 1B 11 102726675 102728866 GRCm39
Protein Domain Hypoxia induced protein, domain 3
protein coding gene MGI:2685767 Higd1c HIG1 domain family, member 1C 15 100262466 100281836 GRCm39
Protein Domain Hypoxia induced protein, domain 3
protein coding gene MGI:1914294 Higd2a HIG1 domain family, member 2A 13 54738044 54738960 GRCm39
Protein Domain Hypoxia induced protein, domain 3
protein coding gene MGI:88574 Cybb cytochrome b-245, beta polypeptide X 9301493 9354005 GRCm39
Process hypoxia-inducible factor-1alpha signaling pathway 3
protein coding gene MGI:1921693 P4htm prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum) 9 108456061 108474866 GRCm39
Function hypoxia-inducible factor-proline dioxygenase activity 3
protein coding gene MGI:1926119 Pdk1 pyruvate dehydrogenase kinase, isoenzyme 1 2 71703568 71734202 GRCm39
Process hypoxia-inducible factor-1alpha signaling pathway 3
protein coding gene MGI:2384308 Pdk3 pyruvate dehydrogenase kinase, isoenzyme 3 X 92808213 92875807 GRCm39
Process hypoxia-inducible factor-1alpha signaling pathway 3
protein coding gene MGI:103223 Vhl von Hippel-Lindau tumor suppressor 6 113600955 113608595 GRCm39
Process hypoxia-inducible factor-1alpha signaling pathway 3
protein coding gene MGI:109474 Commd1 COMM domain containing 1 11 22849728 22934539 GRCm39
Subterm Process negative regulation of hypoxia-inducible factor-1alpha signaling pathway (hypoxia-inducible factor-1alpha signaling pathway) 3
protein coding gene MGI:1920420 Rwdd3 RWD domain containing 3 3 120949047 120965344 GRCm39
Subterm Process positive regulation of hypoxia-inducible factor-1alpha signaling pathway (hypoxia-inducible factor-1alpha signaling pathway) 3
protein coding gene MGI:2443582 Abat 4-aminobutyrate aminotransferase 16 8331293 8439432 GRCm39
Process response to hypoxia 3
protein coding gene MGI:97570 Abcb1a ATP-binding cassette, sub-family B member 1A 5 8710077 8798575 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1352630 Abcc9 ATP-binding cassette, sub-family C member 9 6 142533588 142648041 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1098623 Acaa2 acetyl-CoA acyltransferase 2 18 74912283 74939278 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:87874 Ace angiotensin I converting enzyme 11 105858774 105880790 GRCm39
Process response to hypoxia 3
protein coding gene MGI:2159605 Acot2 acyl-CoA thioesterase 2 12 84034635 84040647 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1338946 Acvrl1 activin A receptor, type II-like 1 15 101026403 101043217 GRCm39
Process response to hypoxia 3
protein coding gene MGI:87916 Ada adenosine deaminase 2 163568504 163592159 GRCm39
Process response to hypoxia 3
protein coding gene MGI:107825 Adam8 a disintegrin and metallopeptidase domain 8 7 139558845 139572475 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1333882 Adam15 ADAM metallopeptidase domain 15 3 89246947 89257589 GRCm39
Process response to hypobaric hypoxia 3
protein coding gene MGI:1096335 Adam17 a disintegrin and metallopeptidase domain 17 12 21373510 21423633 GRCm39
Process response to hypoxia 3
protein coding gene MGI:106675 Adipoq adiponectin, C1Q and collagen domain containing 16 22965286 22976718 GRCm39
Process response to hypoxia 3
protein coding gene MGI:108058 Adm adrenomedullin 7 110226868 110229027 GRCm39
Process response to hypoxia 3
protein coding gene MGI:2685083 Ado 2-aminoethanethiol dioxygenase 10 67380341 67384785 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:99401 Adora1 adenosine A1 receptor 1 134126963 134163169 GRCm39
Process response to hypoxia 3
protein coding gene MGI:87938 Adrb2 adrenergic receptor, beta 2 18 62310887 62313030 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:103202 Adsl adenylosuccinate lyase 15 80832691 80855147 GRCm39
Process response to hypoxia 3
protein coding gene MGI:893592 Ager advanced glycosylation end product-specific receptor 17 34816836 34819910 GRCm39
Process response to hypoxia 3
protein coding gene MGI:87965 Agtr1b angiotensin II receptor, type 1b 3 20368637 20421341 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1339977 Agtrap angiotensin II, type I receptor-associated protein 4 148161518 148172488 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1349419 Aifm1 apoptosis-inducing factor, mitochondrion-associated 1 X 47563821 47602440 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1341886 Ajuba ajuba LIM protein 14 54804929 54815015 GRCm39
Process response to hypoxia 3
protein coding gene MGI:87979 Ak4 adenylate kinase 4 4 101276474 101324192 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:87986 Akt1 thymoma viral proto-oncogene 1 12 112620260 112641266 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:96853 Alad aminolevulinate, delta-, dehydratase 4 62427406 62438155 GRCm39
Process response to hypoxia 3
protein coding gene MGI:87990 Alas2 aminolevulinic acid synthase 2, erythroid X 149330443 149353614 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1353451 Aldh3a1 aldehyde dehydrogenase family 3, subfamily A1 11 61099336 61109244 GRCm39
Process response to hypoxia 3
protein coding gene MGI:2144489 Alkbh5 alkB homolog 5, RNA demethylase 11 60428509 60449338 GRCm39
Process response to hypoxia 3
protein coding gene MGI:88022 Ang angiogenin, ribonuclease, RNase A family, 5 14 51328607 51339462 GRCm39
Process response to hypoxia 3
protein coding gene MGI:104984 Ang2 angiogenin, ribonuclease A family, member 2 14 51432781 51436400 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1201793 Ang3 angiogenin, ribonuclease A family, member 3 14 syntenic NA GRCm39 null Process response to hypoxia 3
protein coding gene MGI:2656551 Ang4 angiogenin, ribonuclease A family, member 4 14 52001349 52011047 GRCm39
Process response to hypoxia 3
protein coding gene MGI:3528599 Ang5 angiogenin, ribonuclease A family, member 5 14 44194526 44200537 GRCm39
Process response to hypoxia 3
protein coding gene MGI:3528602 Ang6 angiogenin, ribonuclease A family, member 6 14 44239121 44243875 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1202890 Angpt2 angiopoietin 2 8 18740279 18791578 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1336887 Angpt4 angiopoietin 4 2 151753130 151787257 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1888999 Angptl4 angiopoietin-like 4 17 33993874 34000549 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1306796 Apaf1 apoptotic peptidase activating factor 1 10 90825173 90918632 GRCm39
Process response to hypoxia 3
protein coding gene MGI:103201 Aqp1 aquaporin 1 6 55313417 55325540 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1333777 Aqp3 aquaporin 3 4 41092724 41098183 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:88071 Arnt aryl hydrocarbon receptor nuclear translocator 3 95341699 95404551 GRCm39
Process response to hypoxia 3
protein coding gene MGI:107188 Arnt2 aryl hydrocarbon receptor nuclear translocator 2 7 83895486 84059201 GRCm39
Process response to hypoxia 3
protein coding gene MGI:96920 Ascl2 achaete-scute family bHLH transcription factor 2 7 142520566 142523001 GRCm39
Process response to hypoxia 3
protein coding gene MGI:109349 Atf2 activating transcription factor 2 2 73646853 73722983 GRCm39
Process intrinsic apoptotic signaling pathway in response to hypoxia 3
protein coding gene MGI:88096 Atf4 activating transcription factor 4 15 80139385 80141742 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:107202 Atm ataxia telangiectasia mutated 9 53350449 53448040 GRCm39
Process response to hypoxia 3
protein coding gene MGI:88108 Atp1b1 ATPase, Na+/K+ transporting, beta 1 polypeptide 1 164264678 164285924 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1924148 B3gat1 beta-1,3-glucuronyltransferase 1 9 26644813 26672646 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1096330 Bad BCL2-associated agonist of cell death 19 6919229 6929267 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:2181667 Bbc3 BCL2 binding component 3 7 16042318 16052130 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:88138 Bcl2 B cell leukemia/lymphoma 2 1 106465908 106642004 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1891828 Becn1 beclin 1, autophagy related 11 101179084 101193112 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1197009 Birc2 baculoviral IAP repeat-containing 2 9 7818228 7837065 GRCm39
Process response to hypoxia 3
protein coding gene MGI:88177 Bmp2 bone morphogenetic protein 2 2 133394079 133404805 GRCm39
Process response to hypoxia 3
protein coding gene MGI:88184 Bmyc brain expressed myelocytomatosis oncogene 2 25596891 25597733 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:109326 Bnip3 BCL2/adenovirus E1B interacting protein 3 7 138492565 138511235 GRCm39
Process intrinsic apoptotic signaling pathway in response to hypoxia 3
protein coding gene MGI:1332659 Bnip3l BCL2/adenovirus E1B interacting protein 3-like 14 67222688 67246326 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:2442836 Brip1 BRCA1 interacting protein C-terminal helicase 1 11 85948964 86092019 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1341265 Camk2d calcium/calmodulin-dependent protein kinase II, delta 3 126389951 126639975 GRCm39
Process response to hypoxia 3
protein coding gene MGI:88259 Camk2g calcium/calmodulin-dependent protein kinase II gamma 14 20784943 20844156 GRCm39
Process response to hypoxia 3
protein coding gene MGI:88264 Capn2 calpain 2 1 182294825 182345173 GRCm39
Process response to hypoxia 3
protein coding gene MGI:2447188 Car9 carbonic anhydrase 9 4 43507026 43513729 GRCm39
Process response to hypoxia 3
protein coding gene MGI:96544 Casp1 caspase 1 9 5298517 5307281 GRCm39
Process response to hypoxia 3
protein coding gene MGI:107739 Casp3 caspase 3 8 47070326 47092724 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1277950 Casp9 caspase 9 4 141520923 141543287 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1351351 Casr calcium-sensing receptor 16 36314058 36382503 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:88271 Cat catalase 2 103284249 103315498 GRCm39
Process response to hypoxia 3
protein coding gene MGI:102709 Cav1 caveolin 1, caveolae protein 6 17306387 17341323 GRCm39
Process response to hypoxia 3
protein coding gene MGI:107570 Cav3 caveolin 3 6 112436466 112449833 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1338013 Cbfa2t3 CBFA2/RUNX1 translocation partner 3 8 123351880 123425848 GRCm39
Process response to hypoxia 3
protein coding gene MGI:88279 Cbl Casitas B-lineage lymphoma 9 44054273 44145346 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:88285 Cbs cystathionine beta-synthase 17 31831602 31856170 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:98259 Ccl2 C-C motif chemokine ligand 2 11 81926403 81928278 GRCm39
Process response to hypoxia 3
protein coding gene MGI:108069 Ccna2 cyclin A2 3 36619014 36626299 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:106185 Ccr2 C-C motif chemokine receptor 2 9 123901987 123913594 GRCm39
Process response to hypoxia 3
protein coding gene MGI:88323 Cd24a CD24a antigen 10 43454433 43460261 GRCm39
Process response to hypoxia 3
protein coding gene MGI:107474 Cd38 CD38 antigen 5 44026153 44069714 GRCm39
Process response to hypoxia 3
protein coding gene MGI:104565 Cdkn1b cyclin dependent kinase inhibitor 1B 6 134897364 134902476 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1261428 Chchd2 coiled-coil-helix-coiled-coil-helix domain containing 2 5 129910002 129916311 GRCm39
Process regulation of cellular response to hypoxia 3
pseudogene MGI:3649942 Chchd2-ps coiled-coil-helix-coiled-coil-helix domain containing 2, pseudogene 4 148152488 148152949 GRCm39
Process regulation of cellular response to hypoxia 3
protein coding gene MGI:87888 Chrna4 cholinergic receptor, nicotinic, alpha polypeptide 4 2 180664104 180685339 GRCm39
Process response to hypoxia 3
protein coding gene MGI:87891 Chrnb2 cholinergic receptor nicotinic beta 2 subunit 3 89660755 89671939 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1914813 Ciao3 cytosolic iron-sulfur assembly component 3 17 25992750 26002306 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1306784 Cited2 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2 10 17598966 17601422 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1346342 Clca1 chloride channel accessory 1 3 144710298 144738537 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1329044 Cldn3 claudin 3 5 135015068 135016326 GRCm39
Process response to hypoxia 3
protein coding gene MGI:88470 Comt catechol-O-methyltransferase 16 18225636 18245602 GRCm39
Process response to hypoxia 3
protein coding gene MGI:108442 Cpeb1 cytoplasmic polyadenylation element binding protein 1 7 80996774 81105207 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:2442640 Cpeb2 cytoplasmic polyadenylation element binding protein 2 5 43390513 43447067 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1098296 Cpt1a carnitine palmitoyltransferase 1a, liver 19 3372334 3435733 GRCm39
Process response to hypoxia 3
protein coding gene MGI:88513 Cr1l complement C3b/C4b receptor 1 like 1 194781019 194813878 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:88498 Crhr1 corticotropin releasing hormone receptor 1 11 104023681 104066349 GRCm39
Process response to hypoxia 3
protein coding gene MGI:88515 Cryaa crystallin, alpha A 17 31896905 31900704 GRCm39
Process response to hypoxia 3
protein coding gene MGI:88516 Cryab crystallin, alpha B 9 50662625 50667936 GRCm39
Process response to hypoxia 3
protein coding gene MGI:2149481 Cygb cytoglobin 11 116536421 116544887 GRCm39
Process response to hypoxia 3
protein coding gene MGI:88588 Cyp1a1 cytochrome P450, family 1, subfamily a, polypeptide 1 9 57595211 57611107 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1926218 Cysltr1 cysteinyl leukotriene receptor 1 X 105617952 105647285 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1917336 Cysltr2 cysteinyl leukotriene receptor 2 14 73263043 73286554 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1197015 Daxx Fas death domain-associated protein 17 34128388 34134564 GRCm39
Process negative regulation of cellular response to hypoxia 3
protein coding gene MGI:1916469 Ddah1 dimethylarginine dimethylaminohydrolase 1 3 145464447 145600032 GRCm39
Process negative regulation of cellular response to hypoxia 3
protein coding gene MGI:1921997 Ddit4 DNA-damage-inducible transcript 4 10 59785497 59787592 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1345277 Ddr2 discoidin domain receptor family, member 2 1 169799876 169938331 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1306782 Dio3 deiodinase, iodothyronine type III 12 110245664 110247531 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1921256 Dnm1l dynamin 1-like 16 16130094 16176823 GRCm39
Process response to hypobaric hypoxia 3
protein coding gene MGI:1261827 Dnmt3a DNA methyltransferase 3A 12 3856007 3964443 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:94919 Dpp4 dipeptidylpeptidase 4 2 62160417 62242575 GRCm39
Process response to hypoxia 3
protein coding gene MGI:99578 Drd1 dopamine receptor D1 13 54205202 54209677 GRCm39
Process negative regulation of cellular response to hypoxia 3
protein coding gene MGI:94924 Drd2 dopamine receptor D2 9 49251927 49319477 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1101357 Ece1 endothelin converting enzyme 1 4 137589548 137692540 GRCm39
Process response to hypoxia 3
protein coding gene MGI:95283 Edn1 endothelin 1 13 42454952 42461466 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:105923 Ednra endothelin receptor type A 8 78389658 78451081 GRCm39
Process response to hypoxia 3
protein coding gene MGI:95295 Egr1 early growth response 1 18 34994260 34998009 GRCm39
Process response to hypoxia 3
protein coding gene MGI:103267 Eif4ebp1 eukaryotic translation initiation factor 4E binding protein 1 8 27750355 27765684 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:95392 Eng endoglin 2 32536607 32572681 GRCm39
Process detection of hypoxia 3
protein coding gene MGI:95393 Eno1 enolase 1, alpha non-neuron 4 150321178 150333336 GRCm39
Process negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway 3
protein coding gene MGI:3648653 Eno1b enolase 1B, retrotransposed 18 48178402 48181446 GRCm39
Process negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway 3
protein coding gene MGI:1276116 Ep300 E1A binding protein p300 15 81470329 81536278 GRCm39
Process response to hypoxia 3
protein coding gene MGI:98277 Epha4 Eph receptor A4 1 77343822 77491725 GRCm39
Process negative regulation of cellular response to hypoxia 3
protein coding gene MGI:95407 Epo erythropoietin 5 137481282 137484078 GRCm39
Process response to hypoxia 3
protein coding gene MGI:95413 Ercc2 excision repair cross-complementing rodent repair deficiency, complementation group 2 7 19115942 19129619 GRCm39
Process response to hypoxia 3
protein coding gene MGI:95414 Ercc3 excision repair cross-complementing rodent repair deficiency, complementation group 3 18 32373357 32403206 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1354385 Ero1a endoplasmic reticulum oxidoreductase 1 alpha 14 45520544 45556029 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:109325 F7 coagulation factor VII 8 13076034 13085809 GRCm39
Process response to hypoxia 3
protein coding gene MGI:95479 Fabp1 fatty acid binding protein 1, liver 6 71176863 71182018 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1917436 Fam162a family with sequence similarity 162, member A 16 35864214 35891931 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:95558 Flt1 FMS-like tyrosine kinase 1 5 147498414 147662821 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1859252 Fmn2 formin 2 1 174329391 174650295 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1915905 Fndc1 fibronectin type III domain containing 1 17 7957401 8046134 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:95574 Fos FBJ osteosarcoma oncogene 12 85520664 85524047 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:102858 Fosl2 fos-like antigen 2 5 32293145 32315186 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1890081 Foxo3 forkhead box O3 10 42057841 42152691 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1919268 Fundc1 FUN14 domain containing 1 X 17422803 17438564 GRCm39
Process response to hypoxia 3
protein coding gene MGI:108520 Fzd4 frizzled class receptor 4 7 89053574 89062341 GRCm39
Process response to hypoxia 3
protein coding gene MGI:95634 Gad2 glutamic acid decarboxylase 2 2 22512262 22583889 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:107516 Gata6 GATA binding protein 6 18 11052510 11085636 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:95781 Gnb1 guanine nucleotide binding protein (G protein), beta 1 4 155575818 155643726 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:109165 Gngt1 guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1 6 3993792 3997436 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:95821 Grin2b glutamate receptor, ionotropic, NMDA2B (epsilon 2) 6 135690231 136150509 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1315197 Hk2 hexokinase 2 6 82702006 82751435 GRCm39
Process response to hypoxia 3
protein coding gene MGI:96163 Hmox1 heme oxygenase 1 8 75820249 75827217 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:109373 Hmox2 heme oxygenase 2 16 4544225 4584606 GRCm39
Process response to hypoxia 3
protein coding gene MGI:109369 Hp1bp3 heterochromatin protein 1, binding protein 3 4 137943607 137971994 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:104720 Hsd11b2 hydroxysteroid 11-beta dehydrogenase 2 8 106245387 106250620 GRCm39
Process response to hypoxia 3
protein coding gene MGI:98817 Hsp90b1 heat shock protein 90, beta (Grp94), member 1 10 86526705 86541308 GRCm39
Process response to hypoxia 3
protein coding gene MGI:96542 Il1a interleukin 1 alpha 2 129141530 129151892 GRCm39
Process response to hypoxia 3
protein coding gene MGI:96552 Il3 interleukin 3 11 54156129 54158103 GRCm39
Process response to hypoxia 3
protein coding gene MGI:107936 Il18 interleukin 18 9 50466127 50493140 GRCm39
Process response to hypoxia 3
protein coding gene MGI:96570 Inhba inhibin beta-A 13 16186436 16206206 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1928268 Ireb2 iron responsive element binding protein 2 9 54771073 54819814 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:96600 Itga2 integrin alpha 2 13 114969617 115068636 GRCm39
Process response to hypoxia 3
protein coding gene MGI:96623 Itpr1 inositol 1,4,5-trisphosphate receptor 1 6 108190057 108528070 GRCm39
Process response to hypoxia 3
protein coding gene MGI:99418 Itpr2 inositol 1,4,5-triphosphate receptor 2 6 146009797 146403721 GRCm39
Process response to hypoxia 3
protein coding gene MGI:96662 Kcna5 potassium voltage-gated channel, shaker-related subfamily, member 5 6 126509514 126512375 GRCm39
Process response to hypoxia 3
protein coding gene MGI:102663 Kcnd2 potassium voltage-gated channel, Shal-related family, member 2 6 21215502 21729804 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1100508 Kcnj8 potassium inwardly-rectifying channel, subfamily J, member 8 6 142510563 142517340 GRCm39
Process response to hypoxia 3
protein coding gene MGI:107501 Kcnj11 potassium inwardly rectifying channel, subfamily J, member 11 7 45746545 45750215 GRCm39
Process response to hypoxia 3
protein coding gene MGI:109366 Kcnk2 potassium channel, subfamily K, member 2 1 188940127 189134470 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1100509 Kcnk3 potassium channel, subfamily K, member 3 5 30745514 30782614 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:99923 Kcnma1 potassium large conductance calcium-activated channel, subfamily M, alpha member 1 14 23342356 24055173 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1095419 Kdm6a lysine (K)-specific demethylase 6A X 18028814 18146175 GRCm39
Process negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway 3
protein coding gene MGI:96683 Kdr kinase insert domain protein receptor 5 76093487 76139118 GRCm39
Process response to hypoxia 3
protein coding gene MGI:104576 Lct lactase 1 128212493 128256055 GRCm39
Process response to hypoxia 3
protein coding gene MGI:104663 Lep leptin 6 29060220 29073875 GRCm39
Process response to hypoxia 3
protein coding gene MGI:96787 Lif leukemia inhibitory factor 11 4207587 4222514 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1352502 Limd1 LIM domains containing 1 9 123307771 123350617 GRCm39
Process response to hypoxia 3
protein coding gene MGI:96794 Lmna lamin A 3 88388455 88413842 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1921392 Lonp1 lon peptidase 1, mitochondrial 17 56921297 56933887 GRCm39
Process response to hypoxia 3
protein coding gene MGI:2137913 Loxl2 lysyl oxidase-like 2 14 69846517 69933283 GRCm39
Process response to hypoxia 3
protein coding gene MGI:104797 Lta lymphotoxin A 17 35422141 35424327 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1346866 Map2k1 mitogen-activated protein kinase kinase 1 9 64093066 64160887 GRCm39
Process negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway 3
protein coding gene MGI:96922 Mb myoglobin 15 76899687 76934868 GRCm39
Process response to hypoxia 3
protein coding gene MGI:96952 Mdm2 transformed mouse 3T3 cell double minute 2 10 117524780 117546663 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:99918 Mecp2 methyl CpG binding protein 2 X 73070198 73129296 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1914999 Mgarp mitochondria localized glutamic acid rich protein 3 51295833 51303968 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:2146020 Mief1 mitochondrial elongation factor 1 15 80118284 80137572 GRCm39
Process cellular response to hypoxia 3
miRNA gene MGI:3618742 Mir199a-2 microRNA 199a-2 1 162045383 162045492 GRCm39
Process cellular response to hypoxia 3
miRNA gene MGI:2676890 Mir214 microRNA 214 1 162050937 162051046 GRCm39
Process cellular response to hypoxia 3
miRNA gene MGI:3629905 Mir668 microRNA 668 12 109701166 109701231 GRCm39
Process cellular response to hypoxia 3
miRNA gene MGI:3718564 Mir874 microRNA 874 13 58170939 58171014 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1929514 Mlst8 MTOR associated protein, LST8 homolog (S. cerevisiae) 17 24692525 24698052 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:97009 Mmp2 matrix metallopeptidase 2 8 93553920 93580049 GRCm39
Process response to hypoxia 3
protein coding gene MGI:101900 Mmp14 matrix metallopeptidase 14 (membrane-inserted) 14 54669055 54679913 GRCm39
Process response to hypoxia 3
protein coding gene MGI:96080 Mst1 macrophage stimulating 1 (hepatocyte growth factor-like) 9 107957635 107962202 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:95691 Mstn myostatin 1 53100799 53107238 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:97173 Mt3 metallothionein 3 8 94879235 94880774 GRCm39
Process response to hypoxia 3
protein coding gene MGI:102504 mt-Co1 mitochondrially encoded cytochrome c oxidase I MT 5328 6872 GRCm39
Process response to hypoxia 3
protein coding gene MGI:102503 mt-Co2 mitochondrially encoded cytochrome c oxidase II MT 7013 7696 GRCm39
Process response to hypoxia 3
protein coding gene MGI:102501 mt-Cytb mitochondrially encoded cytochrome b MT 14145 15288 GRCm39
Process response to hypoxia 3
protein coding gene MGI:101787 mt-Nd1 mitochondrially encoded NADH dehydrogenase 1 MT 2751 3707 GRCm39
Process response to hypoxia 3
protein coding gene MGI:102498 mt-Nd4 mitochondrially encoded NADH dehydrogenase 4 MT 10167 11544 GRCm39
Process response to hypoxia 3
protein coding gene MGI:102496 mt-Nd5 mitochondrially encoded NADH dehydrogenase 5 MT 11742 13565 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1928394 Mtor mechanistic target of rapamycin kinase 4 148533068 148642140 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:97250 Myc myelocytomatosis oncogene 15 61857240 61862223 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:2137495 Myocd myocardin 11 65067387 65160815 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1915419 Ndnf neuron-derived neurotrophic factor 6 65648595 65689307 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:102570 Ndp Norrie disease (pseudoglioma) (human) X 16751760 16778013 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1341799 Ndrg1 N-myc downstream regulated gene 1 15 66801167 66841489 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:97306 Nf1 neurofibromin 1 11 79230519 79472438 GRCm39
Process response to hypoxia 3
protein coding gene MGI:103296 Nfatc3 nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3 8 106785472 106857169 GRCm39
Process response to hypoxia 3
protein coding gene MGI:108420 Nfe2l2 nuclear factor, erythroid derived 2, like 2 2 75505857 75534985 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:2151886 Ngb neuroglobin 12 87144305 87149313 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:97352 Nkx3-1 NK3 homeobox 1 14 69428141 69432107 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1925938 Nol3 nucleolar protein 3 (apoptosis repressor with CARD domain) 8 106002777 106008571 GRCm39
Process negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway 3
protein coding gene MGI:1855692 Nono non-POU-domain-containing, octamer binding protein X 100473080 100492199 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:2154441 Nop53 NOP53 ribosome biogenesis factor 7 15671760 15680033 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:97361 Nos2 nitric oxide synthase 2, inducible 11 78811613 78851052 GRCm39
Process response to hypoxia 3
protein coding gene MGI:97363 Notch1 notch 1 2 26347914 26393834 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1101358 Npepps aminopeptidase puromycin sensitive 11 97096668 97171464 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:97369 Nppc natriuretic peptide type C 1 86594015 86598295 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1352456 Nr4a2 nuclear receptor subfamily 4, group A, member 2 2 56996845 57014018 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1339639 Ogt O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase) X 100683666 100727957 GRCm39
Process negative regulation of cellular response to hypoxia 3
protein coding gene MGI:97438 Oprd1 opioid receptor, delta 1 4 131838037 131871797 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:2665170 P2rx2 purinergic receptor P2X, ligand-gated ion channel, 2 5 110487678 110491078 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1097160 P2rx3 purinergic receptor P2X, ligand-gated ion channel, 3 2 84828927 84867806 GRCm39
Process response to hypoxia 3
protein coding gene MGI:97464 P4hb prolyl 4-hydroxylase, beta polypeptide 11 120451124 120464079 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1339975 Pak1 p21 (RAC1) activated kinase 1 7 97437748 97561588 GRCm39
Process response to hypoxia 3
protein coding gene MGI:97501 Pck1 phosphoenolpyruvate carboxykinase 1, cytosolic 2 172994866 173001067 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1860611 Pdlim1 PDZ and LIM domain 1 (elfin) 19 40210683 40260060 GRCm39
Process response to hypoxia 3
protein coding gene MGI:104629 Penk preproenkephalin 4 4133536 4138815 GRCm39
Process response to hypoxia 3
protein coding gene MGI:105095 Pgf placental growth factor 12 85213411 85224559 GRCm39
Process response to hypoxia 3
protein coding gene MGI:97555 Pgk1 phosphoglycerate kinase 1 X 105230706 105247305 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:102520 Phb2 prohibitin 2 6 124689299 124693913 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1922019 Pik3cb phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta 9 98920455 99022264 GRCm39
Process negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway 3
protein coding gene MGI:1346036 Pin1 peptidyl-prolyl cis/trans isomerase, NIMA-interacting 1 9 20563335 20575008 GRCm39
Process response to hypoxia 3
protein coding gene MGI:3649546 Pin1rt1 peptidyl-prolyl cis/trans isomerase, NIMA-interacting 1, retrogene 1 2 104544271 104546724 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1916193 Pink1 PTEN induced putative kinase 1 4 138040720 138053618 GRCm39
Process negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway 3
protein coding gene MGI:97610 Plat plasminogen activator, tissue 8 23247743 23272860 GRCm39
Process response to hypoxia 3
protein coding gene MGI:97611 Plau plasminogen activator, urokinase 14 20886728 20893453 GRCm39
Process response to hypoxia 3
protein coding gene MGI:892877 Pld2 phospholipase D2 11 70430890 70448936 GRCm39
Process response to hypoxia 3
protein coding gene MGI:2387630 Plekhn1 pleckstrin homology domain containing, family N member 1 4 156305913 156312999 GRCm39
Process response to hypoxia 3
protein coding gene MGI:109604 Plk3 polo like kinase 3 4 116985852 116991160 GRCm39
Process positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia 3
protein coding gene MGI:99907 Plod1 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 4 147994210 148021224 GRCm39
Process response to hypoxia 3
protein coding gene MGI:104662 Pml promyelocytic leukemia 9 58125359 58157069 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1926321 Postn periostin, osteoblast specific factor 3 54268530 54298458 GRCm39
Process response to hypoxia 3
protein coding gene MGI:104740 Ppara peroxisome proliferator activated receptor alpha 15 85619184 85687020 GRCm39
Process response to hypoxia 3
protein coding gene MGI:101884 Ppard peroxisome proliferator activator receptor delta 17 28451715 28520446 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:97747 Pparg peroxisome proliferator activated receptor gamma 6 115337912 115467360 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:97749 Ppia peptidylprolyl isomerase A 11 6365867 6369817 GRCm39
Process response to hypoxia 3
protein coding gene MGI:2145955 Prkaa1 protein kinase, AMP-activated, alpha 1 catalytic subunit 15 5173343 5211380 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:97596 Prkcb protein kinase C, beta 7 121888327 122233625 GRCm39
Process response to hypoxia 3
protein coding gene MGI:97599 Prkce protein kinase C, epsilon 17 86475213 86965347 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1206587 Prl4a1 prolactin family 4, subfamily a, member 1 13 28200195 28207531 GRCm39
Process response to hypoxia 3
protein coding gene MGI:894281 Prl8a2 prolactin family 8, subfamily a, member 2 13 27529656 27538199 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1316652 Prmt2 protein arginine N-methyltransferase 2 10 76043060 76073699 GRCm39
Process response to hypoxia 3
protein coding gene MGI:109583 Pten phosphatase and tensin homolog 19 32734977 32803560 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1097156 Ptgis prostaglandin I2 (prostacyclin) synthase 2 167033725 167082524 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:97798 Ptgs2 prostaglandin-endoperoxide synthase 2 1 149975851 149983978 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:104908 Ptk2b PTK2 protein tyrosine kinase 2 beta 14 66390706 66518501 GRCm39
Process response to hypoxia 3
protein coding gene MGI:97830 Pygm muscle glycogen phosphorylase 19 6434438 6448494 GRCm39
Process response to hypoxia 3
protein coding gene MGI:108016 Rad21 RAD21 cohesin complex component 15 51825636 51855143 GRCm39
Process response to hypoxia 3
protein coding gene MGI:97847 Raf1 v-raf-leukemia viral oncogene 1 6 115595530 115653596 GRCm39
Process response to hypoxia 3
protein coding gene MGI:97895 Reg1 regenerating islet-derived 1 6 78402966 78405651 GRCm39
Process response to hypoxia 3
protein coding gene MGI:104897 Rest RE1-silencing transcription factor 5 77413338 77434279 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1913464 Rgcc regulator of cell cycle 14 79526190 79539075 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:107926 Rock2 Rho-associated coiled-coil containing protein kinase 2 12 16944896 17037824 GRCm39
Process regulation of cellular response to hypoxia 3
protein coding gene MGI:104661 Rora RAR-related orphan receptor alpha 9 68561068 69295528 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1921620 Rptor regulatory associated protein of MTOR, complex 1 11 119493731 119790402 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1915835 Rtn4 reticulon 4 11 29642947 29694331 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:99659 Ryr1 ryanodine receptor 1, skeletal muscle 7 28702765 28824599 GRCm39
Process response to hypoxia 3
protein coding gene MGI:99685 Ryr2 ryanodine receptor 2, cardiac 13 11567988 12121831 GRCm39
Process response to hypoxia 3
protein coding gene MGI:2135958 Scap SREBF chaperone 9 110162356 110214017 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1924233 Scfd1 Sec1 family domain containing 1 12 51424296 51496887 GRCm39
Process response to hypoxia 3
protein coding gene MGI:98248 Scn2a sodium channel, voltage-gated, type II, alpha 2 65451115 65597791 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1914175 Sdhd succinate dehydrogenase complex, subunit D, integral membrane protein 9 50507657 50515112 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:892014 Sfrp1 secreted frizzled-related protein 1 8 23901518 23939648 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:2135607 Sirt1 sirtuin 1 10 63154784 63174814 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1927664 Sirt2 sirtuin 2 7 28466192 28488086 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1922637 Sirt4 sirtuin 4 5 115616069 115622784 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:95755 Slc2a1 solute carrier family 2 (facilitated glucose transporter), member 1 4 118965942 118994527 GRCm39
Process response to hypoxia 3
protein coding gene MGI:95758 Slc2a4 solute carrier family 2 (facilitated glucose transporter), member 4 11 69833365 69839014 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1860103 Slc2a8 solute carrier family 2, (facilitated glucose transporter), member 8 2 32863002 32872095 GRCm39
Process response to hypoxia 3
protein coding gene MGI:96285 Slc6a4 solute carrier family 6 (neurotransmitter transporter, serotonin), member 4 11 76889429 76923166 GRCm39
Process response to hypoxia 3
protein coding gene MGI:107956 Slc8a1 solute carrier family 8 (sodium/calcium exchanger), member 1 17 81680534 82045806 GRCm39
Process response to hypoxia 3
protein coding gene MGI:107976 Slc8a3 solute carrier family 8 (sodium/calcium exchanger), member 3 12 81244689 81379954 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:102462 Slc9a1 solute carrier family 9 (sodium/hydrogen exchanger), member 1 4 133097022 133151013 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1345279 Slc11a2 solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2 15 100285779 100322090 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1927073 Slc29a1 solute carrier family 29 (nucleoside transporters), member 1 17 45896126 45910532 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1201674 Smad3 SMAD family member 3 9 63554049 63665276 GRCm39
Process response to hypoxia 3
protein coding gene MGI:894293 Smad4 SMAD family member 4 18 73772080 73836851 GRCm39
Process response to hypoxia 3
protein coding gene MGI:98352 Sod2 superoxide dismutase 2, mitochondrial 17 13226726 13237006 GRCm39
Process response to hypoxia 3
protein coding gene MGI:103181 Sod3 superoxide dismutase 3, extracellular 5 52521146 52527080 GRCm39
Process response to hypoxia 3
protein coding gene MGI:98366 Sox4 SRY (sex determining region Y)-box 4 13 29132902 29137682 GRCm39
Process response to hypoxia 3
protein coding gene MGI:98397 Src Rous sarcoma oncogene 2 157265828 157313758 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:106658 Srf serum response factor 17 46859255 46867101 GRCm39
Process response to hypoxia 3
protein coding gene MGI:103038 Stat3 signal transducer and activator of transcription 3 11 100777632 100830447 GRCm39
Process regulation of cellular response to hypoxia 3
protein coding gene MGI:109131 Stc1 stanniocalcin 1 14 69266738 69278850 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1316731 Stc2 stanniocalcin 2 11 31309441 31320061 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1099440 Suv39h1 suppressor of variegation 3-9 1 X 7927410 7940999 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1890396 Suv39h2 suppressor of variegation 3-9 2 2 3456852 3476068 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1341163 Tacc3 transforming, acidic coiled-coil containing protein 3 5 33815472 33836339 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1351652 Tbl2 transducin (beta)-like 2 5 135178288 135192727 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:98664 Tek TEK receptor tyrosine kinase 4 94627526 94763213 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1202709 Tert telomerase reverse transcriptase 13 73775030 73797962 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:107810 Tfam transcription factor A, mitochondrial 10 71061294 71074110 GRCm39
Process response to hypoxia 3
protein coding gene MGI:98822 Tfrc transferrin receptor 16 32427738 32451612 GRCm39
Process response to hypoxia 3
protein coding gene MGI:98725 Tgfb1 transforming growth factor, beta 1 7 25386427 25404502 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:98726 Tgfb2 transforming growth factor, beta 2 1 186354989 186438186 GRCm39
Process response to hypoxia 3
protein coding gene MGI:98727 Tgfb3 transforming growth factor, beta 3 12 86103519 86125815 GRCm39
Process detection of hypoxia 3
protein coding gene MGI:98735 Th tyrosine hydroxylase 7 142446516 142453732 GRCm39
Process response to hypoxia 3
protein coding gene MGI:2442752 Tigar Trp53 induced glycolysis regulatory phosphatase 6 127062079 127086520 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:2139220 Tm9sf4 transmembrane 9 superfamily member 4 2 153003223 153052386 GRCm39
Process response to hypoxia 3
protein coding gene MGI:99682 Tmbim6 transmembrane BAX inhibitor motif containing 6 15 99290828 99307930 GRCm39
Process negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway 3
protein coding gene MGI:104798 Tnf tumor necrosis factor 17 35418357 35420983 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1913150 Trem2 triggering receptor expressed on myeloid cells 2 17 48653429 48659304 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:98823 Trh thyrotropin releasing hormone 6 92219042 92221631 GRCm39
Process response to hypoxia 3
protein coding gene MGI:98834 Trp53 transformation related protein 53 11 69471185 69482699 GRCm39
Process intrinsic apoptotic signaling pathway in response to hypoxia 3
protein coding gene MGI:1926945 Trpv4 transient receptor potential cation channel, subfamily V, member 4 5 114760213 114796482 GRCm39
Process response to hypoxia 3
protein coding gene MGI:102548 Tsc2 TSC complex subunit 2 17 24814790 24851604 GRCm39
Process response to hypoxia 3
protein coding gene MGI:98872 Twist1 twist basic helix-loop-helix transcription factor 1 12 34007670 34009828 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1929468 Txn2 thioredoxin 2 15 77799251 77813194 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1860276 Ubqln1 ubiquilin 1 13 58323970 58363467 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1932970 Ucn3 urocortin 3 13 3990688 3995349 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:109354 Ucp2 uncoupling protein 2 (mitochondrial, proton carrier) 7 100142565 100148832 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1099787 Ucp3 uncoupling protein 3 (mitochondrial, proton carrier) 7 100122198 100135639 GRCm39
Process response to hypoxia 3
protein coding gene MGI:99542 Usf1 upstream transcription factor 1 1 171238875 171246327 GRCm39
Process response to hypoxia 3
protein coding gene MGI:1918722 Usp19 ubiquitin specific peptidase 19 9 108367806 108379536 GRCm39
Process regulation of cellular response to hypoxia 3
protein coding gene MGI:1346329 Uts2 urotensin 2 4 151081554 151086267 GRCm39
Process response to hypoxia 3
protein coding gene MGI:2177651 Vasn vasorin 16 4457805 4468666 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:103178 Vegfa vascular endothelial growth factor A 17 46327919 46343295 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:106199 Vegfb vascular endothelial growth factor B 19 6959841 6965019 GRCm39
Process response to hypoxia 3
protein coding gene MGI:109124 Vegfc vascular endothelial growth factor C 8 54530567 54639489 GRCm39
Process response to hypoxia 3
protein coding gene MGI:108037 Vegfd vascular endothelial growth factor D X 163156374 163185646 GRCm39
Process response to hypoxia 3
protein coding gene MGI:98935 Vldlr very low density lipoprotein receptor 19 27193884 27231631 GRCm39
Process cellular response to hypoxia 3
protein coding gene MGI:1915086 Wdr83 WD repeat domain containing 83 8 85801664 85807375 GRCm39
Process response to hypoxia 3
protein coding gene MGI:2141920 Wtip WT1 interacting protein 7 33808968 33832693 GRCm39
Process response to hypoxia 3
protein coding gene MGI:99137 Xrcc1 X-ray repair complementing defective repair in Chinese hamster cells 1 7 24246124 24272863 GRCm39
Process response to hypoxia 3
lncRNA gene MGI:1916199 Zfas1 zinc finger, NFX1-type containing 1, antisense RNA 1 2 166904854 166907782 GRCm39
Process regulation of hypoxia-induced intrinsic apoptotic signaling pathway 3
protein coding gene MGI:107946 Zfp36l1 zinc finger protein 36, C3H type-like 1 12 80154534 80159787 GRCm39
Process cellular response to hypoxia 3

3.2 Gene Differentiation Volcano

Here, we use Wilcoxon Test to compute gene differential expression (DE). The statistical significance was cut-off by log2(Fold Change) > 1 or log2(Fold Change) < -1 and p_value < 0.05.

The ischemia-related gene are highlighted in volcano plot by purple color, while hypoxia-related genes are marked in green. No ischemia-hypoxia-overlap gene is found in DE.

3.2.1 Microglia (4 hours), tBHP vs PBS

logfoldchanges pvals
Selplg 7.804862 0.0000000
Apoe -3.794668 0.0000000
C1qa 3.027765 0.0000000
Slc17a7 1.934162 0.0001875
Serpinf1 -1.611794 0.0127633
Nnat -1.523112 0.0002573
Ctss 1.202592 0.0003786
Cd9 -1.000260 0.0068657

3.2.2 Microglia(24 hours), tBHP vs PBS

logfoldchanges pvals
Tmem119 9.655052 0.0000000
Cx3cr1 9.207951 0.0000000
Csf1r 7.521422 0.0000000
C1qa 6.288658 0.0000000
Ctss 4.346459 0.0000035
Camk2a 3.978816 0.0000000
Bin1 2.346426 0.0000000
Apoe 1.898717 0.0000196
Ctsb 1.771201 0.0000000
Plp1 1.656879 0.0022404
Cd14 1.628826 0.0000000
Cspg5 1.620137 0.0000051
Aldh1l1 1.425023 0.0046848
Trem2 1.414192 0.0002061
Sncg 1.364001 0.0245285
Itgam 1.336048 0.0000000
Casp8 1.334647 0.0017914
Rbfox3 1.271873 0.0096435
Inpp5d 1.213771 0.0000029
Cd9 1.205624 0.0023450
Spi1 1.185843 0.0004712
Tcerg1 1.140319 0.0018037
Sla 1.096807 0.0000018
Zbtb20 1.081156 0.0009113
Nptx1 1.074096 0.0166972
Lrpprc 1.068678 0.0109181
Sharpin 1.065369 0.0195681
Abi3 1.056846 0.0000005
Syn1 1.051837 0.0025161
Ctsc 1.000470 0.0000616

3.2.3 Endothelial (4 hours), tBHP vs PBS

logfoldchanges pvals
Icam1 4.321182 0.0000005
Vcam1 1.990366 0.0359665
Slc17a7 1.944467 0.0000000
Agt -1.849056 0.0004980
Nnat -1.548581 0.0000001
Pecam1 1.424326 0.0000000
Nptxr 1.219218 0.0154648
Klf2 -1.188156 0.0000000
Cldn5 1.106118 0.0166088
Camk2a 1.005879 0.0001490

3.2.4 Endothelial (24 hours), tBHP vs PBS

logfoldchanges pvals
Bsg 14.207772 0.0000000
Cldn5 8.383662 0.0000000
Apoe 3.879512 0.0000000
Camk2a 3.245064 0.0000000
App 2.708132 0.0000033
Flt1 2.425270 0.0000000
Pecam1 2.256013 0.0000000
Mfsd2a 2.185250 0.0000000
Ctnnb1 1.970689 0.0000000
Gfap 1.806280 0.0000364
Kcnq1 1.715021 0.0091454
Plp1 1.607371 0.0013174
Cspg5 1.545747 0.0000000
Cx3cl1 1.531581 0.0000054
Nos3 1.520198 0.0000000
Xdh 1.502282 0.0000000
Nptxr 1.472057 0.0000195
Ppp1r1b 1.443743 0.0173912
Klf2 1.395932 0.0000000
Fn1 1.385187 0.0003460
Sema3g 1.272809 0.0486582
Arc -1.256589 0.0003183
Stard8 1.242842 0.0001185
Zbtb20 1.223462 0.0000000
Rgs5 1.216236 0.0000001
Lef1 1.192588 0.0000001
Tcerg1 1.179086 0.0141037
Ngrn 1.148234 0.0371505
Cdh5 1.141593 0.0000000
Pcdhgc3 1.121873 0.0000000
Grb2 1.105423 0.0009515
Rbfox3 1.103138 0.0068434
Syn1 1.100524 0.0012414
Bin1 1.090345 0.0012565
Syp 1.079221 0.0020913
Fam131a 1.045174 0.0279760
Lmna 1.044754 0.0000058
Dnm1 1.039805 0.0158126

4. Capillary Localization

4.1 Capillary marker: Pecam1

4.2 Capillary Cell Count

Since Pecam1 is capillary gene marker, we picked up endothelial cells that express log-normalized Pecam1 expression > 1, and consider them as capillary cells.

Capillary Cell Count
id cell.count
0 tBHP_4 743
3 tBHP_24 731
1 PBS_4 374
2 PBS_24 329

4.3 Defferentiation Volcano

4.3.1 Capillary, 4 hours, tBHP vs PBS

logfoldchanges pvals
Icam1 3.367107 0.0028161
Agt -1.842217 0.0025396
Slc17a7 1.755432 0.0000049
Nnat -1.531274 0.0000035
Klf2 -1.198818 0.0000029

4.3.2 Capillary, 24 hours, tBHP vs PBS

logfoldchanges pvals
Bsg 16.433660 0.0000000
Cldn5 11.126303 0.0000000
Apoe 5.104093 0.0000000
Camk2a 3.493571 0.0000000
App 3.254875 0.0000112
Flt1 2.968592 0.0000000
Mfsd2a 2.625379 0.0000000
Fn1 2.292427 0.0000043
Gfap 2.277436 0.0000160
Ctnnb1 2.137518 0.0000000
Pecam1 1.965661 0.0000000
Nos3 1.731574 0.0000000
Ntng2 1.706747 0.0411791
Klf2 1.691222 0.0000000
Trpm4 1.665571 0.0191938
Nptxr 1.616628 0.0000585
Syp 1.610862 0.0011809
Xdh 1.608494 0.0000000
Cx3cl1 1.570906 0.0000736
Cspg5 1.566026 0.0000017
Kcnq1 1.559081 0.0219258
Tcerg1 1.550006 0.0148341
Hpca 1.538213 0.0069025
Stard8 1.525962 0.0000401
Dnm1 1.466346 0.0031463
Lef1 1.389383 0.0000002
Rgs5 1.354013 0.0000014
Pdgfa 1.328179 0.0170938
Fam131a 1.322172 0.0439337
Rbfox3 1.271759 0.0134575
Eno2 1.252816 0.0177234
Mtor 1.234967 0.0002744
Erbb2 1.213557 0.0120796
Lmna 1.209302 0.0000229
Cdh5 1.195409 0.0000055
Bin1 1.182991 0.0031035
Zbtb20 1.168966 0.0000002
Grb2 1.167131 0.0043860
Plp1 1.156247 0.0058271
Syn1 1.093356 0.0075128
Adam10 1.042479 0.0035064

Supplement: Abbreviation

Cell types & Regions

Astro, Astrocyte;

ABC, arachnoid barrier cells;

BAM, border-associated macrophages;

BLA, Basolateral amygdala;

CB, cerebellum;

CGE, caudal ganglionic eminence;

CHOR, choroid plexus;

CNU, cerebral nuclei;

CR, Cajal–Retzius;

CT, corticothalamic;

CTX, cerebral cortex;

CTXsp, cortical subplate;

DC, dendritic cells;

DCO, dorsal cochlear nucleus;

DG, dentate gyrus;

EA, extended amygdala;

Endo, endothelial cells;

ENT, Entorhinal area;

ENTl, Entorhinal area, lateral part;

Epen, ependymal;

EPI, epithalamus;

ET, extratelencephalic;

GC, granule cell;

HB, hindbrain;

HPF, hippocampal formation;

HY, hypothalamus;

HYa, anterior hypothalamic;

IMN, immature neurons;

IT, intratelencephalic;

L6b, layer 6b;

LGE, lateral ganglionic eminence;

LH, lateral habenula;

LSX, lateral septal complex;

MB, midbrain;

MGE, medial ganglionic eminence;

MH, medial habenula;

MM, medial mammillary nucleus;

MY, medulla;

NN, non-neuronal;

NP, near-projecting;

NT, non-telencephalon;

OB, olfactory bulb;

OEC, olfactory ensheathing cells;

OLF, olfactory areas;

Oligo, oligodendrocytes;

OPC, oligodendrocyte precursor cells;

P, pons;

PAL, pallidum;

Peri, pericytes;

PIR, piriform cortex;

SMC, smooth muscle cells;

STR, striatum;

TE, telencephalon;

TH, thalamus;

UBC, unipolar brush cells;

VLMC, vascular leptomeningeal cells.

Neurotransmitter types

Chol, cholinergic;

Dopa, dopaminergic;

GABA, GABAergic;

Glut, glutamatergic;

Glyc, glycinergic;

Hist, histaminergic;

Nora, noradrenergic;

Sero, serotonergic

ADP, anterodorsal preoptic nucleus

AHN, anterior hypothalamic nucleus

ARH, arcuate hypothalamic nucleus

CLI, central linear nucleus raphe

CUN, cuneiform nucleus

DMH, dorsomedial nucleus of the hypothalamus

DMX, dorsal motor nucleus of the vagus nerve

IF, interfascicular nucleus raphe

LHA, lateral hypothalamic area

MDRN, medullary reticular nucleus

MPN, medial preoptic nucleus

MPO, medial preoptic area

MV, medial vestibular nucleus

NTS, nucleus of the solitary tract

PAG, periaqueductal grey

PARN, parvicellular reticular nucleus

PB, parabrachial nucleus

PBG, parabigeminal nucleus

PGRN, paragigantocellular reticular nucleus

PGRNd, paragigantocellular reticular nucleus, dorsal part

PH, posterior hypothalamic nucleus

PMv, ventral premammillary nucleus

PPN, pedunculopontine nucleus

PVa, periventricular hypothalamic nucleus, anterior part

PVHd, paraventricular hypothalamic nucleus, descending division

PVi, periventricular hypothalamic nucleus, intermediate part

PVpo, periventricular hypothalamic nucleus, preoptic part

PVR, periventricular region

RAmb, midbrain raphe nuclei

RL, rostral linear nucleus raphe

SBPV, subparaventricular zone

SNc, substantia nigra, compact part

SPIV, spinal vestibular nucleus

TMv, tuberomammillary nucleus, ventral part

VII, facial motor nucleus

VMPO, ventromedial preoptic nucleus

VTA, ventral tegmental area

ZI, zona incerta.